Vasospastic angina (VA) is a functional disease of the coronary artery and occurs in an angiographically normal coronary artery. However, it may also occur with coronary artery stenosis. We investigated the effect of coronary artery stenosis on clinical outcomes in VA patients. Study data were obtained from a prospective multicenter registry that included patients who had symptoms of VA. Patients were classified into two groups according to presence of significant coronary artery stenosis. Among 1920 patients with VA, 189 patients were classified in the “significant stenosis” group. The one-year composite clinical events rate was significantly higher in the significant stenosis group than in the “no significant stenosis” group (5.8% vs. 1.4%, respectively; p < 0.001). Additionally, the prevalence of ACS was significantly greater in the “significant stenosis” group (4.8% vs. 0.9%, respectively; p < 0.001). After propensity score matching, the adverse effects of significant stenosis remained. In addition, significant stenosis was independently associated with a 6.67-fold increased risk of ACS in VA patients. In conclusion, significant coronary artery stenosis can increase the adverse clinical outcomes in VA patients at long-term follow-up. Clinicians should manage traditional risk factors associated with atherosclerosis and control vasospasm as well as reduce the burden of atherosclerosis.